Contemporary Selective Breeding. Plant Edition.

In an effort to address the naivete and sentimentality that people have about agriculture, we continue our look at contemporary selective breeding. After looking at the state of the art of dairy cow breeding, I thought we’d take a look at some recent articles about the state of the art in non-GMO plant breeding.

The story starts with the arrival of some seeds from habaneros that mutated in such away that they produced little to no capsaicin. Michael Mazourek started crossing them with other plants to try to create a pepper that had a habenero’s subtle, smoky flavor without the brutal and distracting heat. By running the genome of the plant and isolating the alleles responsible for the traits he was seeking he was able to skip step of waiting for plants to produce fruit to test if they were expressing those traits.

Mazourek belongs to a new generation of plant breeders who combine traditional farming with rapid genetic analysis to create more flavorful, colorful, shapely and nutritious fruits and vegetables. These modern plant breeders are not genetic engineers; in most cases they do not directly manipulate plant DNA in the lab. Rather, they sequence the genomes of many different kinds of plants to build databases that link various versions of genes—known as alleles—to distinct traits. Then, they peek inside juvenile plants to examine the alleles that are already there before choosing which ones to grow in the field and how best to mate one plant with another. In some cases breeders can even analyze the genetic profiles of individual seeds and subsequently select which to sow and which to disregard, saving them a great deal of time and labor.

Plant breeders have, of course, always used the best tools available to them. But in the last 10 years or so they have been able to approach their work in completely new ways in part because genetic sequencing technology is becoming so fast and cheap. “There’s been a radical change in the tools we use,” says Jim Myers of Oregon State University, who has been a plant breeder for more than 20 years and recently created an eggplant-purple tomato. “What is most exciting to me, and what I never thought I would be doing, is going in and looking at candidate genes for traits. As the price of sequencing continues to drop, it will become more and more routine to do sequences for every individual population of plants you’re working with.”

. . . In part to circumvent the controversy surrounding GMOs, fruit and vegetable breeders at both universities and private companies have been turning to an alternative way of modifying the food we eat: a sophisticated approach known as marker-assisted breeding that marries traditional plant breeding with rapidly improving tools for isolating and examining alleles and other sequences of DNA that serve as “markers” for specific traits. Although these tools are not brand-new, they are becoming faster, cheaper and more useful all the time. “The impact of genomics on plant breeding is almost beyond my comprehension,” says Shelley Jansky, a potato breeder who works for both the U.S. Department of Agriculture (USDA) and the University of Wisconsin–Madison. “To give an example: I had a grad student here five years ago who spent three years trying to identify DNA sequences associated with disease resistance. After hundreds of hours in the lab he ended up with 18 genetic markers. Now I have grad students who can get 8,000 markers for each of 200 individual plants within a matter of weeks. Progress has been exponential in last five years.”

. . . Mills can look for these markers in cantaloupe seeds before deciding which ones to plant thanks to a group of cooperative and largely autonomous robots, some of which are housed in Monsanto’s molecular breeding lab at its vegetable research and development headquarters in Woodland, Calif. First, a machine known as a seed chipper shaves off a small piece of a seed for DNA analysis, leaving the rest of the kernel unharmed and suitable for sowing in a greenhouse or field. Another robot extracts the DNA from that tiny bit of seed and adds the necessary molecules and enzymes to chemically glue fluorescent tags to the relevant genetic sequences, if they are there. Yet another machine amplifies the number of these glowing tags in order to measure the light they emit and determine whether a gene is present. Monsanto’s seed chippers can run 24 hours a day and the whole system can deliver results to breeders within two weeks.

This example from the article is striking in that it shows Monsanto actively helping out local (east coast) vegetable farmers.

Fresh broccoli consumed the same day it was harvested is completely different from typical supermarket fare, Bjorkman says—it’s tender, with a mellow vegetative flavor, a hint of honeysuckle and no sharp aftertaste. Trucking broccoli from California to other parts of the country requires storing the vegetable on ice in the dark for days. With no light, photosynthesis halts, which means that cells stop making sugars. Rapidly dropping temperatures rupture cell walls, irrevocably weakening the plant’s structure and diminishing its firmness. When the broccoli is thawed, various enzymes and molecules that escaped their cells bump into one another and trigger a sequence of chemical reactions, some of which degrade both nutritional and flavorful compounds. Giving farmers in the east broccoli they can grow and sell locally solves all these problems. In a separate effort to boost the nutritional value of broccoli, Monsanto released Beneforte broccoli, which has been bred to contain extra high levels of glucoraphanin, a compound that some evidence indicates may fight bacteria and cancer. You can find the florets at some Whole Foods and States Bros.

It’s telling that there seem to be no safety concerns for the random mutation not previously existing in nature in those habaneros that Michael Mazourek was sent. It’s a novel gene that hasn’t been field tested for environmental concerns, it hasn’t undergone composition analysis, or testing for allergens. If breeders using genetic engineering to move one single gene to express a well understood protein into a crop all those things and a decade of testing would be necessary. Go figure.

A recent piece by Nova was about genetic engineering, but again, I thought the most interesting part was it’s portrayal of how specific and directed contemporary breeding is.

De Jong produced the plants in the same old, laborious way that his father did before him. He collected pollen from a plant that produces potatoes that fry as potato chips should and then sprinkled the pollen on the flower of a potato plant that resists viruses. If the resulting potatoes bear their parents’ finest features—and none of the bad ones—De Jong will bury them in the ground next year and test their mettle against a common potato virus. If they survive—and are good for frying and eating—he and his team will repeat this for 13 years to ensure that problematic genes did not creep in during the initial cross.

Each year, the chance of failure is high. Potatoes that resist viruses, for example, often have genes that make them taste bitter. Others turn an unappetizing shade of brown when fried. If anything like that happens, De Jong will have to start from scratch. Tedious as it is, he loves the work. Kicking up dirt in the furrows that cascade along the hillsides of upstate New York, he says, “I’m never stressed in the potato fields.”

De Jong has some serious cred in the agriculture world. Not only was his father a potato breeder, he’s also descended from a long line of farmers. The potato farmers he works with appreciate this deeply, along with his commitment to the age-old craft of producing new potato varieties through selective breeding. They even advocated on his behalf during his hiring and when he was up for tenure at Cornell, a school with a long history of agriculture research. “All of our farmers like Walter,” says Melanie Wickham, the executive secretary of the Empire State Growers organization in Stanley, New York. Often, he’s in the fields in a big hat, she says. Other times “you’ll see him in the grocery store, looking over the potatoes.”

De Jong has been working with farmers long enough to know that our food supply is never more than a step ahead of devastating insect infestations and disease. Selective breeders like De Jong work hard to develop resistant crops, but farmers still have to turn to chemical pesticides, some of which are toxic to human health and the environment. De Jong enjoys dabbing pollen from plant-to-plant the old-fashioned way, but he knows that selective breeding can only do so much.
seedlings

So while De Jong still devotes most of his time to honing his craft, he has recently begun to experiment in an entirely different way, with genetic engineering. To him, genetic engineering represents a far more exact way to produce new varieties, rather than simply scrambling the potato genome’s 39,000 genes the way traditional breeding does. By inserting a specific fungus-defeating gene into a tasty potato, for example, De Jong knows he could offer farmers a product that requires fewer pesticides.

“We want to make food production truly sustainable,” De Jong says, “and right now I cannot pretend that it is.”

. . . I first encountered De Jong on April 4, when he sat on a panel about GMOs in New York City hosted by the advocacy groups GMO Free NY and the Wagner Food Policy Alliance. The modest awkwardness that endears him to farmers didn’t charm the audience. As De Jong explained how scientists create GMOs, they began to murmur, lost amidst De Jong’s scientific jargon and meandering delivery.

De Jong did, however, liven up during a discussion in which Jean Halloran, a member of the panel from the Consumer’s Union, suggested that farmers in the developing world could ditch pesticides, not use GMOs, and increase yields. “We favor a knowledge-based approach rather than a chemical-based approach to increasing production,” Halloran had said.

De Jong did not find this solution realistic and asked, “Do you want to be the African farmer who has to apply insecticide every week—really nasty stuff—without protective equipment?” The question hung in the air for a second, and the panelist beside him repeated the no-chemical mantra.

Weeks later, De Jong tells me the panel opened his eyes. He was shocked at how people who don’t live near farms feel entitled to advise farmers, especially on environmental matters. “There is a romantic notion of environmentalism, and then there is actual environmentalism,” De Jong says. “Farmers are very conscious of the environment. They want to hand off their operation to their kids and their kids’ kids, so they maintain the land the best they can while doing what they need to do in order to sell their harvest,” he says. “My guess is that the majority of people who are anti-GM live in cities and have no idea what stewardship of the land entails.”

“I find it so tragic that, by and large, crop biotechnologists and farmers want to reduce their pesticide use, and yet the method we think is most sustainable and environmentally friendly has been dismissed out of hand.” He pauses as he recalls the event and says, “There is no scientific justification for it—it is just as if there is a high priest who decided, ‘Thou shalt not be GMO.’ ”

DeJong is very clear about the traits his potatoes are going to end up with. He’s going to get to where wants to go. What he doesn’t understand is why he shouldn’t just skip to the good part.

P.S. Wired has an interesting piece on the vegetables that Monsanto has developed using these techniques. I’ve been using those BellaFina peppers for some time with out realizing they were a Monsanto product. They are great. Cheap and convenient. I used one pepper at a time, mostly in my morning eggs.

13 responses to “Contemporary Selective Breeding. Plant Edition.”

Disclaimer up front – I work for Monsanto, the shennanigans below are entirely of my own design and not a nefarious plan by the writer of my paycheck to disseminate information or appear witty… (also, cross posting this from elsewhere at the behest of (I assume…) the same Marc)

While true that many genes are shared… the sharing isn’t perfect (I’d almost bet that there isn’t a single shared gene between a human and banana that is identical, for instance – even at the protein level (it’s easy to differ at the nucleotide leveldue to the redundancy of the genetic code, it’s slightly less easy to differ at the amino-acid level (although utterly possible as proteins tend to have big hunks of sequence which do not so much at all (at least not in so far as exact sequence is necessarily important).

It’s also not clear to me what is meant by “which pairing makes the best transfer” – I’ve been involved in many meetings deciding upon a gene source for a given gene – first and foremost, at least in industry for food/feed based products… animals are out (for entirely unscientific reasons), then you tend to want to avoid allergenic species (wheat particularly… again, totally unscientific – mostly a business decision based on cost of deregulation) and then you’ll consider the environment in which the protein might find itself, whether you want the gene regulated in the same manner as the native version plus the evolutionary similarity between species – a gene from soy, going into soy (for instance) is far more likely to retain any in vivo regulation, whereas if you were to source the same gene functionality from say, a random soil bacterium – it is highly unlikely that the gene would be regulated by the machinery found in your average soy cell (RNAi for instance operates in planta, often within the coding sequence, thus a gene from a closely related species is far more likely to retain any silencing etc than one from a distantly related species)